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Novel Reference Transcriptomes for the Sponges Carteriospongia

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Novel Reference Transcriptomes for the Sponges Carteriospongia bioRxiv preprint doi: https://doi.org/10.1101/2020.06.26.156463; this version posted June 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Novel reference transcriptomes for the 2 sponges Carteriospongia foliascens and 3 Cliona orientalis and associated algal 4 symbiont Gerakladium endoclionum 5 Brian W. Strehlow*1,2,3,4,5,6, Mari-Carmen Pineda5,6, Carly D. Kenkel5,7, Patrick Laffy5, Alan Duckworth5,6, 6 Michael Renton2,8, Peta L. Clode2,3,4, Nicole S Webster5,6,9 7 *corresponding author 8 Author emails, respectively: [email protected], [email protected], [email protected], 9 [email protected], [email protected], [email protected], [email protected], 10 [email protected] 11 12 1 Current address: Department of Biology, Nordcee, University of Southern Denmark, Campusvej 55, 5230 13 Odense, Denmark 14 2School of Biological Sciences, University of Western Australia, 35 Stirling Hwy, Crawley WA 6009, Australia 15 3Centre for Microscopy, Characterisation and Analysis, University of Western Australia, 35 Stirling Hwy, 16 Crawley WA 6009, Australia 17 4Oceans Institute, University of Western Australia, 35 Stirling Hwy, Crawley WA 6009, Australia 18 5Australian Institute of Marine Science, PMB No 3, Townsville MC, Queensland 48106 Western Australian 19 Marine Science Institution, Crawley, WA, Australia 20 6Western Australian Marine Science Institution, 35 Stirling Hwy, Crawley WA 6009, Australia 21 7Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, 22 CA 90089, USA 23 8School of Agriculture and Environment, University of Western Australia, 35 Stirling Hwy, Crawley WA 6009, 24 Australia 25 9Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of 26 Queensland, Brisbane, QLD, Australia 27 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.26.156463; this version posted June 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 28 Abstract 29 Transcriptomes from sponges are important resources for studying the stress responses of these 30 ecologically important filter feeders, the interactions between sponges and their symbionts, and the 31 evolutionary history of metazoans. Here, we generated reference transcriptomes for two common and 32 cosmopolitan Indo-Pacific sponge species: Carteriospongia foliascens and Cliona orientalis. We also created 33 a reference transcriptome for the primary symbiont of C. orientalis – Gerakladium endoclionum. To ensure 34 a full repertoire of transcripts were included, clones of each sponge species were exposed to a range of 35 individual stressors: decreased salinity, elevated temperature, elevated suspended sediment 36 concentrations, sediment deposition and light attenuation. RNA extracted from all treatments was pooled 37 for each species, using equal concentrations from each clone. Sequencing of pooled RNA yielded 409 and 38 418 million raw reads for C. foliascens and C. orientalis holobionts (host and symbionts), respectively. Reads 39 underwent quality trimming before assembly with Trinity. Assemblies were filtered into sponge-specific or, 40 for G. endoclionum, symbiont-specific assemblies. Assemblies for C. foliascens, C. orientalis, and G. 41 endoclionum contained 67,304, 82,895, and 28,670 contigs, respectively. Contigs represented 15,248- 42 37,344 isogroups (~genes) per assembly, and N50s ranged 1,672-4,355 bp. Gene ortholog analysis verified a 43 high level of completeness and quality for sponge-specific transcriptomes, with an average 93% of core 44 EuKaryotic Orthologous Groups (KOGs) and 98% of single-copy metazoan core gene orthologs identified. 45 The G. endoclionum assembly was partial with only 56% of core KOGs and 32% of single-copy eukaryotic 46 core gene orthologs identified. These reference transcriptomes are a valuable resource for future 47 molecular research aimed at assessing sponge stress responses. 48 Keywords 49 Porifera, transcriptome, sponge, Cliona orientalis, Carteriospongia foliascens, Gerakladium endoclionum bioRxiv preprint doi: https://doi.org/10.1101/2020.06.26.156463; this version posted June 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 50 Data Description 51 Sponges, phylum Porifera, represent one of the oldest lineages of multicellular animals [1], hence 52 investigating the transcriptomes of different sponge species can provide insight into the evolution of 53 metazoans and their gene expression profiles. Furthermore, sponges have an uncertain future in the face of 54 global climate change [2,3] as well as local stressors including coastal development, altered hydrological 55 processes, and increased runoff of nutrients, pesticides and sediments [4–7]. Transcriptomic analysis of 56 sponges that have been exposed to different environmental conditions would improve our understanding 57 of the sponge molecular stress response pathways and enhance our ability to effectively manage these 58 ecologically important filter feeders. Although there are approximately 9,000 described sponge species [8], 59 to date only ~35 species have published transcriptomes [9-25] and only ~10 have published genomes 60 [10,16,26–29]. 61 In this study, we assembled the transcriptomes of two common and widely distributed Indo-pacific sponge 62 species – Carteriospongia foliascens and Cliona orientalis. Both are emerging model species that have been 63 extensively used to study the physiological and ecological effects of environmental stressors on sponges 64 [30–37]. C. foliascens and C. orientalis are only the second members of their respective orders 65 (Dictyoceratida and Clionaida) to have a reference transcriptome sequenced. Whilst both C. foliascens and 66 C. orientalis host diverse populations of bacterial symbionts, e.g. [32], C. orientalis additionally hosts an 67 abundant population of eukaryotic Symbiodiniaceae, Gerakladium endoclionum [38,39], which comprises 68 up to 96% of its algal symbiont community [37]. We used sequences generated from the C. orientalis 69 holobiont, i.e. host and symbiont, to construct a partial reference transcriptome for Gerakladium 70 endoclionum. Matching host and symbiont transcriptomes provide a valuable tool to understand the 71 holobiont response to changing environmental conditions and determine the cause-effect pathways for 72 declining host health with environmental change. These data contribute substantially to available poriferan 73 genetic resources and advance the development of these two sponge species as model systems for field 74 and laboratory studies. bioRxiv preprint doi: https://doi.org/10.1101/2020.06.26.156463; this version posted June 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 75 Methods 76 Samples and sequencing 77 Samples of C. foliascens and C. orientalis were collected in May 2015 from Fantome Is. (S 18°41.028 E 146° 78 30.706) and Pelorus Is. (S 18°32.903' E 146° 29.172'), respectively, in the central Great Barrier Reef under 79 permits G12/35236.1 and G13/35758.1. As C. orientalis is a bioeroding sponge that encrusts and erodes 80 coral skeletons, five C. orientalis cores (~5 cm in diameter) were collected using an air-drill from a single 81 individual, i.e. cloned, growing on a dead colony of Porites sp. An individual of C. foliascens was cut (cloned) 82 into five pieces as in [32]. Sponges were healed and acclimated under natural light and flow-through 83 seawater for 4 weeks before experiments were performed. 84 In order to capture the full complement of gene expression within the reference transcriptomes, sponges 85 were subjected to five different treatments at the Australian Institute of Marine Science (AIMS) National 86 Sea Simulator: i) decreased salinity, ii) elevated temperature, iii) elevated suspended sediment 87 concentrations (SSCs) and sediment deposition, iv) light attenuation and v) no stress control. Sponge clones 88 were used across all treatments to control for genotype, i.e. one genotype was used per species. Two 89 clones of each species were used for each treatment. In the salinity stress treatment, salinity was 90 decreased from 35 to 22 parts per thousand (ppt) by gradually adding flow-through reverse osmosis (RO) 91 water to the system. Salinity was held constant at 22 ppt for 2 d with flow-through seawater maintained at 92 600 mL min-1. In the heat stress treatment, sponges were exposed to a constant temperature of 32.5˚C for 93 1 d using methods described in [32]. In the sediment treatment, sponges were exposed to elevated SSCs at 94 200 mg L-1 for 1 d as in [40,41], using sediments described therein. In the deposition experiment, 95 sedimentation was approximately 40 mg cm-2, measured using SedPods [42] and sponges were left covered 96 with sediment for 1 d. In the light attenuation treatment, sponges were kept in complete darkness for 2 d. 97 Immediately after each treatment, a sample of sponge tissue (~1 cm3) was flash frozen in liquid nitrogen 98 and stored at -80˚C [43] for RNA extraction and sequencing (RNA-seq). After exposure to the decreased bioRxiv preprint doi: https://doi.org/10.1101/2020.06.26.156463; this version posted June 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
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